Great that notmuch alone works.
For the set -x, edit the mutt-open script, and add a "set -x" line just after the "#!/bin/bash" line. Then, re-run the "mutt-open MESSAGE_ID" test (using a message-id that you know notmuch will find) and send me the output, e.g. via a link obtained from http://paste.debian.net
It will probably be very long, so it's best to redirect all the output to a file, and upload that file to paste.d.n
Stefano Zacchiroli at 2013-11-22T11:55:42Z